Bent DNA sites in mammalian replication origins
Balani, V.A.1; Takeda, K.I.1; Fiorini, A.2; Fernandez, M.A.1
1Depto. de Biologia Celular e Genética, DBC, Universidade Estadual de Maringá, UEM, Paraná, Brasil. e-mail: mafernandez@uem.br; 2Centro Universitário de Maringá – CESUMAR, Paraná, Brasil
Intrinsic bent DNA sites associated to replication initiation regions (IR) were described in several organisms. In lower eukaryotes as Saccaharomyces cerevisiae it is know that intrinsic DNA bent sites are conserved in ARS consensus. For DHFR (dihydrofolate reductase) locus it was related that the ori-b origin requires four specific elements for its full activity, including intrinsically bent DNA. We have detected in Chinese hamster AMPD2 (Adenylate deaminase 2) amplicon, intrinsic bent DNA sites in the GNAI3-GNAT2 intergenic region (where is located an IR, oriGNAI3) and near the oriB. Recently we also related the existence of the intrinsic bent DNA sites in an IR from Rhynchosciara americana DNA puff C3 amplicon. The aim of our work was to map intrinsic bent DNA sites by computational analysis of segments containing IR which sequence and localization was described previously. The sequences analyzed in this work were the Chinese hamster AMPD2 and DHFR amplicons and in humans the c-myc gene segment, the b-globin locus and the lamin B2 gene segment. The sequences were analyzed using the Map15a and 3D15m1 software based on the wedge model for curvature. The analyzed parameters were ENDS ratio and Roll angle using a 200 bp window width and a 10 bp step. The results indicate that the DNA segments show ENDS ratio peaks between 1.2 and 1.8 localized ~1500 bp upstream and/or downstream from the IR. The Roll angle indicated that the IR segments could be divided into two groups. The first is composed by origins that present negative Roll values near their putative core, which includes the oriGNAI3, ori-b, lamin B2 and c-myc IRs. Except for the IR present in lamin B2 segment, all the others IRs have implicated in genic amplification. The second group is composed by the b-globin IR and oriB and oriC from the AMPD2 amplicon, which showed positive Roll angle values. The 2D modeling of all these IR showed a discrete curvature in the origin core, but when the modeling was performed with a more representative ENDS ratio peak observed near each IR, the curvature was greatly pronounced. These results indicate the presence of significant sequence-directed bent sites in IRs sites and add the helical parameters/structural features to improve the knowledge on the functional mammalian replication origins.
Supported by: CAPES; CNPq; TWAS; FINEP; Fundação Araucária; Complexo de Centrais de Apoio a Pesquisa, COMCAP-UEM
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